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DNA Microarray Data Analysis Workshop - Thailand
The course will be held from August 23 - 27, 2004 (incl.)
Lectures and exercises will take place at Room no. 127, BIOTEC Building, Thailand Science Park, Pathumthani, Thailand
Recommended book: A Biologist's Guide to Analysis of DNA Microarray Data, by professor Steen Knudsen
An introduction to R is available on-line.
Beginner's Guide to UNIX is available on-line.
Course Programme
 Monday, August 23
- 9.00-9.30
- Introduction to the workshop
Hanne Jarmer & H. Bjørn Nielsen, CBS
- 9:30-10.00
- Coffee Break
- 10.00-11.00
- Overview of gene expression and DNA microarray technology.
Different technologies - advantages and disadvantages
(Lecture notes)
Hanne Jarmer, CBS
- 11:00-11.15
- Coffee Break
- 11.15-12.00
- Discussion of student's motivations and projects
Hanne Jarmer & H. Bjørn Nielsen, CBS
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Analysis of the cell cycle (case story)
(Lecture notes)
H. Bjørn Nielsen, CBS
- 14.00-14.15
- Coffee Break
- 14.15-15.30
- Short introduction to the statistical language R
(Lecture notes) ,
(Exercise),
(The harder exercise)
H. Bjørn Nielsen, CBS
- 15.30-15.45
- Test of the day
- 15.45->
- Preparation of student's data
Hanne Jarmer & H. Bjørn Nielsen, CBS
Tuesday, August 24
- 9.00-9.45
- Experimental design and setup
(Lecture notes)
Hanne Jarmer & H. Bjørn Nielsen, CBS
- 9:45-10.00
- Coffee Break
- 10.00-11.30
-
Probe design (incl. exercise)
(Lecture notes)
Nielsen.et.al.03.pdf
OligoWiz II
Introduction to regular expressions
H. Bjørn Nielsen, CBS
- 11.30-12.00
- Analysis of probe performance
(Lecture notes)
H. Bjørn Nielsen, CBS
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Sample preparation, hybridization, scanning and image analysis
(Lecture notes)
Hanne Jarmer, CBS
- 14:00-14.15
- Coffee Break
- 14.15-15.15
- Arabidopsis transcriptomics (case story)
(Petersen.et.al.00.pdf)
H. Bjørn Nielsen, CBS
- 15.15-15.30
- Coffee Break
- 15.30-15.45
- Test of the day
Wednesday, August 25
- 9.00-11.00
- Normalization
(Lecture notes),
(Exercise)
H. Bjørn Nielsen, CBS
- 11:00-11.15
- Coffee Break
- 11.15-12.00
- Statistical analysis of microarray data
(Lecture notes)
Hanne Jarmer, CBS
- 12.00-13.00
- Lunch Break
- 13.00-15.00
- Statistical analysis of microarray data
(Exercise)
Hanne Jarmer, CBS
- 15.00-15.15
- Coffee Break
- 15.15-16.00
- Aspergillus nidulans expression study (case story)
(Lecture notes)
H. Bjørn Nielsen, CBS
- 16.00-16.15
- Test of the day
Thursday, August 26
- 9.00-10.30
- PCA, Clustering and Classification
(Lecture notes)
H. Bjørn Nielsen, CBS
- 10:30-11.00
- Coffee Break
- 11.00-12.00
- PCA, Clustering and Classification
(Exercise)
H. Bjørn Nielsen, CBS
- 12.00-13.00
- Lunch Break
- 13.00-13.45
- Transcriptome analysis of the TnrA regulon in Bacillus subtilis (case story)
Pathway analysis and regulatory networks
(Lecture notes)
Hanne Jarmer, CBS
- 13:45-14.00
- Coffee Break
- 14.00-15.15
- Reverse engineering of regulatory networks
(Exercise)
Hanne Jarmer, CBS
- 15:15-15.30
- Coffee Break
- 15.30-16.00
- Promoter analysis, in silico
(Lecture notes) ,
(Demo server)
H. Bjørn Nielsen, CBS
- 16.15-16.30
- Test of the day
Friday, August 27
- 9.00-10.00
- Lecture and demonstration: CodeLink Bioarrays - A Reliable Microarray-based Assay for Accurate and Precise Expression Profiling and Genotyping Studies
Amersham
- 10:00-10.15
- Coffee Break
- 10:15-12.30
- Automated analysis of array data
(Exercise)
Hanne Jarmer, CBS
- 12.30-13.30
- Lunch Break
- 13.30-14.00
- Microarray projects in Thailand - an overview
Supapon Cheevadhanarak, BIOTEC
- 14.00-16.00
- Round table discussion
- 16.00-16.15
- Final discussion and course evaluation
- 17.00
End of course
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